Computational Pipeline for Large-Scale Gene Network Analysis. GNLab (Gene Network virtual Laboratory) is a novel bioinformatics tool for the large-scale analysis of gene regulatory networks (GRNs). This C++ command-line tool supports the analysis of both the static structure and dynamic behaviour of a GRN. GNLab is developed to support the design and implementation of large-scale repeatable computational experimentations on GRNs.

GNLab consists of separable components for network generation, simulation, analysis, visualization, comparison and inference. Through the use of a user-defined script, these components can be piped together to construct a pipeline of GRN analysis. Each component can be invoked by a command-line option.

GNLab Features:
1. Network Generation
Three network growth models are available in GNLab. A random network can be generated by the Erdos-Renyi model (-r), the Scale-free model (-f), or the Charleston-Ho model (-g).

2. Network Visualization
GNLab can produce input files for GraphViz, GEOMI and Cytoscape. This functionality can be invoked by the command-line option -v.

3. Network Simulation
Using the Hill's kinetics, the gene expression pattern of a GRN can be simulated either deterministically or stochastically. Data for the time-series gene expression profile can be generated by invoking command-line option -t. The simulated data is stored in a text file with a ".data" extension.

4. Network Analysis
The static structure of a GRN can be quantified by a collection of network topological features. A set of 11 topological features is calculated in GNLab.

5. Network Comparison
The topological similarity between two networks with the same number of nodes can be calculated in GNLab. A network comparison is invoked through the command-line option -c. A one-line summary of topological differences between the two networks is outputed to the console.

6. Network Inference
GNLab does not perform network inference directly. However, it allows the microarray dataset it generates to be converted into the input format of ARACNe and Banjo. This process is invoked by the command-line option -d.

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